PXD053370

PXD053370 is an original dataset announced via ProteomeXchange.

Title	Hemicellulose utilisation in Flavobacterium
Description	The plant hemicellulose xyloglucan (XyG) is secreted from the roots of numerous plant species, including cereals, and contributes towards soil aggregate formation in terrestrial systems. Whether XyG represents a key nutrient for plant-associated bacteria is unclear. The phylum Bacteroidota are abundant in the plant microbiome and provide several beneficial functions for their host. However, the metabolic and genomic traits underpinning their success remain poorly understood. Here, we employed whole-cell proteomics to determine the molecular mechanisms responsible for xyloglucan utilisation in two model Flavobacterium species, Flavobacterium johnsoniae DSM2064 and Flavobacterium sp. OSR005. We identified the occurrence of a distinct and conserved gene cluster, referred to as the Xyloglucan Utilisation Loci (XyGUL). Flavobacterium XyGUL is a hybrid of the molecular machinery found in gut Bacteroides spp., Cellvibrio japonicus, and the plant pathogen Xanthomonas. Combining protein biochemistry, computational modelling and phylogenetics, we identified a mutation in the enzyme required for initiating hydrolysis of the XyG polysaccharide, an outer membrane endoxyloglucanase glycoside hydrolase family 5 subfamily 4 (GH5_4), which enhances activity towards XyG.
HostingRepository	PRIDE
AnnounceDate	2025-05-07
AnnouncementXML	Submission_2025-05-06_20:15:01.370.xml
DigitalObjectIdentifier	https://dx.doi.org/10.6019/PXD053370
ReviewLevel	Peer-reviewed dataset
DatasetOrigin	Original dataset
RepositorySupport	Supported dataset by repository
PrimarySubmitter	Andrew Bottrill
SpeciesList	scientific name: Flavobacterium sp. F52; NCBI TaxID: 1202532;
ModificationList	monohydroxylated residue; iodoacetamide derivatized residue
Instrument	Orbitrap Fusion

Revision	Datetime	Status	ChangeLog Entry
0	2024-06-24 12:31:15	ID requested
⏵ 1	2025-05-06 20:15:02	announced

10.6019/PXD053370;

Martin H, Rogers LA, Moushtaq L, Brindley AA, Forbes P, Quinton AR, Murphy ARJ, Hipperson H, Daniell TJ, Ndeh D, Amsbury S, Hitchcock A, Lidbury IDEA, Metabolism of hemicelluloses by root-associated Bacteroidota species. ISME J, 19(1):(2025) [pubmed]

10.1093/ismejo/wraf022;

submitter keyword: Flavobacterium, Warwick_RTP, Hemicellulose, xyloglucan

Dr Ian Lidbury
contact affiliation	School of Biosciences University of Sheffield Western Bank Sheffield S10 2TN United Kingdom
contact email	i.lidbury@sheffield.ac.uk
lab head
Andrew Bottrill
contact affiliation	University of Warwick
contact email	a.r.bottrill@gmail.com
dataset submitter

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PRIDE project URI

• PRIDE
  1. PXD053370
     1. Label: PRIDE project
     2. Name: Hemicellulose utilisation in Flavobacterium